It communicates with you ECU to adjust boost, A/F ratio, etc.
It uses off-the-shelf (OTS) maps that are designed to be safe and reliable. Take a look at the link I posted earlier to see a comparison of stock vs. StageII. If you get a Protune (which you'll need some form of EM for, which includes the AP), you'll be putting down numbers comparable to a stock STi.
Basically they have pre-configured maps for fuel/timing/boost etc. based on different stages of mods done to your car
Ya its a way to tune (flash) your ecu to manage the bolt ons your car has and maximize the gain in hp/tq you get, without having to go to a tuner.
Eventually you would want to get a pro tune, because the maps are "cookie cutter" and not every car is exactly the same or reacts the same to mods. I have essentialy what you have, but I am putting on a VF39 Turbo, Fuel Pump, Injectors and run a cobb map temporarily...until I can get a pro tune to create a custom map for me to run based on my mods and my car.
Go to Cobb site and it will break down their stages and generally what mods correspond to what stage you are in.